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What do the src tags of the images / js files etc. look like? Presumably they are relative paths, when requesting assets for a page the relative paths will be relative to the current URL, if you are using pretty URLs that are multiple 'directories' deep (i.e. you have slashes in them) the assets will be searched for relative to this point.

So let's say we have an index.php file in your server root, along with a js folder which contains jquery.js. In index.php you have <script src="js/jquery.js"></script>, this will work just fine, requesting the javascript file from /js/jquery.js but if you rewrite the URL /multi-level/path-url to index.php, It will attempt to load the javascript file from /multi-level/js/jquery.js, which obviously wont exist.

Long story short, use path relative to root (start with a forward slash), or absolute paths.

What do the src tags of the images / js files etc. look like? Presumably they are relative paths, when requesting assets for a page the relative paths will be relative to the current URL, if you are using pretty URLs that are multiple 'directories' deep (i.e. you have slashes in them) the assets will be searched for relative to this point.

So let's say we have an index.php file in your server root, along with a js folder which contains jquery.js. In index.php you have <script src="js/jquery.js"></script>, this will work just fine, requesting the javascript file from /js/jquery.js but if you rewrite the URL /multi-level/path-url to index.php, It will attempt to load the javascript file from /multi-level/js/jquery.js, which obviously wont exist.

Long story short, use path relative to root (start with a forward slash), or absolute paths.